SelfCross#

class pybrops.breed.prot.mate.SelfCross.SelfCross(progeny_counter=0, family_counter=0, rng=None, **kwargs)[source]#

Bases: MatingProtocol

Class implementing mating protocols for self-fertilization.

Constructor for the concrete class SelfCross.

Parameters:

progeny_counter (Integral) – Progeny counter. This helps create progeny names.
family_counter (Integral) – Family counter. This helps label groups of progenies as originating from the same family.
rng (numpy.random.Generator, numpy.random.RandomState) – Random number source.
kwargs (dict) – Additional keyword arguments.

Methods

mate

Self-fertilize individuals.

Attributes

`family_counter`	Description for property family_counter.
`nparent`	Number of parents the mating protocol requires.
`progeny_counter`	Description for property progeny_counter.
`rng`	Random number generator.

property family_counter: Integral#: Description for property family_counter.

mate(pgmat, xconfig, nmating, nprogeny, miscout=None, nself=0, **kwargs)[source]#

Self-fertilize individuals.

Example crossing diagram:

         pgmat
           │                sel = [A,...]
           A
     ┌─────┴─────┐          nmating = 2
     A           A
  ┌──┴──┐     ┌──┴──┐       initial self, nprogeny = 2
S0(A) S0(A) S0(A) S0(A)     cross pattern finished.
  │     │     │     │       s = 2
S1(A) S1(A) S1(A) S1(A)     first self
  │     │     │     │
S2(A) S2(A) S2(A) S2(A)     second self, final result

Parameters:

pgmat (DensePhasedGenotypeMatrix) – A DensePhasedGenotypeMatrix containing candidate breeding individuals.
xconfig (numpy.ndarray) –
Array of shape (ncross,nparent) containing indices specifying a cross configuration. Each index corresponds to an individual in pgmat.

Where:
- ncross is the number of crosses to perform.
- nparent is the number of parents required for a cross.
Indices are organized as follows:
- All indices are self parents.
Example:
```
xconfig = [[ 1 ],
           [ 3 ],
           [ 2 ],
           ...,
           [ S ]]
self = [1, 3, 2, ..., S]
```
ncross (numpy.ndarray) – Number of cross patterns to perform.
nprogeny (numpy.ndarray) – Number of progeny to generate per cross.
miscout (dict, None, default = None) – Pointer to a dictionary for miscellaneous user defined output. If dict, write to dict (may overwrite previously defined fields). If None, user defined output is not calculated or stored.
s (int, default = 0) – Number of generations of single seed descent post-cross pattern.
kwargs (dict) – Additional keyword arguments to be passed to constructor for the output DensePhasedGenotypeMatrix.

Returns:

out – A DensePhasedGenotypeMatrix of progeny.

Return type:

DensePhasedGenotypeMatrix

property nparent: Integral#: Number of parents the mating protocol requires.

property progeny_counter: Integral#: Description for property progeny_counter.

property rng: Generator | RandomState#: Random number generator.